The invention provides a microbe-enzyme composite preparation used for restoring water in an urban and rural polluted river, and its preparation method. The urban and rural polluted river restoration microbe-enzyme composite preparation is characterized in that the microbe mainly comprises 30-60% of Bacillus licheniformis, 25-35% of a nitrobacterium, and 15-35% of pseudomonas putida; and the composite enzyme mainly comprises 40-60% of a protease, 15-25% of an amylase and 25-35% of a cellulase. The optimized microbe is compounded with the composite enzyme to prepare the microbe-enzyme composite preparation against water of different pollution degrees, the addition amount of the microbe is 1-5g/m<3>, and the addition amount of the composite enzyme is 0.01-0.05g/m<3>. The microbe-enzyme composite preparation is added to the urban and rural polluted river to carry out microbial reinforced restoration with aeration as an auxiliary measure, can effectively improve defects of low microbe metabolism activity, low environmental tolerance, short retention time in the polluted water and the like existing in the prior art, and has a substantial water purifying effect.